Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
183
datasets available to search
ShareScore release 0.9.0
Dataset results
183 results for “secretome”
Storage conditions affect the composition of the lyophilized secretome of multipotent mesenchymal stromal cells - graphs
<p>Figures for artcile Rogulska, O., Vackova, I., Prazak, S. <em>et al.</em> Storage conditions affect the composition of the lyophilized secretome of multipotent mesenchymal stromal cells. <em>Sci Rep</em> 14, 10243 (2024). https://doi.org/10.1038/s41598-024-60787-z</p> <p><span>Fig. 1. Preservation of the growth factors and cytokines in the lyophilized MSC-derived conditioned medium after 3 months of storage at different temperatures (N=3). Data is presented as Median (Q1; Q3). * - the values are significantly (p<0.05) lower compared to the -80°C group; # - the values are significantly (p<0.05) lower compared to the -20°C group. The values are related to non-lyophilized MSC-sec stored for the same time (3 months) in a frozen state at −80°C.</span></p> <p><span> </span><span>Fig. 2. The preservation of growth factors and cytokines in the lyophilized MSC-derived conditioned medium after 30 months of storage at different temperatures (N=3). Data is presented as Median (Q1; Q3). * - the values are significantly (p<0.05) lower compared to the -80°C group; # - the values are significantly (p<0.05) lower compared to the -20°C group; ° - the values are significantly (p<0.05) lower compared to the 4°C group. The values are related to non-lyophilized MSC-sec stored for the same time (30 months) in a frozen state at −80°C.</span></p> <p><span> </span><span>Fig. 3. The preservation levels of the whole lyophilized MSC-sec cocktail, determined as the median of the preservation values for each of the MSC-sec components. The v</span><span>alues are related to non-lyophilized MSC-sec stored for the same time in a frozen state at −80°C.</span></p>
The secretome atlas of two mouse models of progeria
<p>Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disease caused by nuclear envelope alterations that lead to accelerated aging and premature death. Several studies have linked health and longevity to cell-extrinsic mechanisms, highlighting the relevance of circulating factors in the aging process as well as in age related diseases. We performed a global plasma proteomic analysis in two preclinical progeroid models (<em>Lmna<sup>G609G/G609G</sup></em> and <em>Zmpste24<sup>-/-</sup></em> mice) using aptamer-based proteomic technology. Pathways related to the extracellular matrix, growth factor response and calcium ion binding were among the most enriched in the proteomic signature of progeroid samples compared to controls. Despite the global down-regulation trend found in the plasma proteome of progeroid mice, several proteins associated with cardiovascular disease, the main cause of death in HGPS, were up-regulated. We also developed a chronological age predictor using plasma proteome data from a cohort of healthy mice (aged 1-30 months), that reported an age acceleration when applied to progeroid mice, indicating that these mice exhibit an ‘old’ plasma proteomic signature. Furthermore, when compared to naturally-aged mice, a great proportion of differentially expressed circulating proteins in progeroid mice were specific to premature aging, highlighting secretome-associated differences between physiological and accelerated aging. This is the first large-scale profiling of the plasma proteome in progeroid mice, which provides an extensive list of candidate circulating plasma proteins as potential biomarkers and/or therapeutic targets for further exploration and hypothesis generation in the context of both physiological and premature aging.</p>
Endoplasmic Reticulum Associated Aminopeptidase 2 (ERAP2) Is Released in the Secretome of Activated MDMs and Reduces in vitro HIV-1 Infection
<p><strong>Background:</strong> Haplotype-specific alternative splicing of the endoplasmic reticulum (ER) aminopeptidase type 2 (ERAP2) gene results in either full-length (FL, haplotype A) or alternatively spliced (AS, haplotype B) mRNA. HapA/HapA homozygous (HomoA) subjects show a reduced susceptibility to HIV-1 infection, probably secondary to the modulation of the antigen processing/presenting machinery. ERAP1 was recently shown to be secreted from the plasma membrane in response to activation; we investigated whether ERAP2 can be released as well and if the secreted form of this enzyme retains its antiviral function.</p> <p><strong>Methods:</strong> Human monocyte derived macrophages (MDMs) were differentiated from peripheral blood mononuclear cells (PBMCs) isolated from 6 HomoA healthy controls and stimulated with IFNγ and LPS. ERAP2-FL secretion was evaluated by mass spectrometry. PBMCs (14 HomoA and 16 HomoB) and CD8-depleted PBMCs (CD8<sup>−</sup>PBMCs) (4 HomoA and 4 HomoB) were <em>in vitro</em> HIV-infected in the absence/presence of recombinant human ERAP2-FL (rhERAP2) protein; p24 viral antigen quantification was used to assess viral replication. IFNγ and CD69 mRNA expression, as well as the percentage of perforin-producing CD8+ T Lymphocytes, were analyzed 3 and 7-days post <em>in vitro</em> HIV-1-infection, respectively. The effect of rhERAP2 addition in cell cultures on T cell apoptosis, proliferation, activation, and maturation was evaluated as well on 24 h-stimulated PBMCs.</p> <p><strong>Results:</strong> ERAP2 can be secreted from human MDMs in response to IFNγ/LPS stimulation. Notably, the addition of rhERAP2 to PBMC and CD8<sup>−</sup>PBMC cultures resulted in the reduction of viral replication, though these differences were statistically significant only in PBMCs (<em>p</em> < 0.05 in both HomoA and HomoB). This protective effect was associated with an increase in IFNγ and CD69 mRNA expression and in the percentage of perforin-expressing CD107<sup>+</sup>CD8<sup>+</sup> cells. RhERAP2 addition also resulted in an increase in CD8<sup>+</sup> activated lymphocyte (CD25<sup>+</sup>HLA<sup>−</sup>DRII<sup>+</sup>) and Effector Memory/Terminally differentiated CD8<sup>+</sup> T cells ratio.</p> <p><strong>Conclusions:</strong> This is the first report providing evidence for the release of ERAP2 in the secretome of immunocompetent cells. Data herein also indicate that exogenous ERAP2-FL exerts its protective function against HIV-1 infection, even in HomoB subjects who do not genetically produce it. Presumably, this defensive extracellular feature is only partially dependent on immune system modulation.</p>
Unravelling potential virulence factor candidates in Xanthomonas citri. subsp. citri by secretome analysis
<p>Citrus canker is a major disease affecting citrus production in Brazil. Its mainly caused by <em>Xanthomonas citri </em>subsp. <em>citri</em> strain 306 pathotype A (Xac). We analysed the differential expression of proteins secreted by wild type Xac and an asymptomatic mutant for <em>hrpB4</em> (<em>ΔhrpB4</em>) grown in Nutrient Broth (NB) and a medium mimicking growth conditions in the plant (XAM1). This allowed the identification of 55 secreted proteins, of which 37 were secreted by both strains when cultured in XAM1. In this secreted protein repertoire, the following stand out: Virk, Polyphosphate-selective porin, Cellulase, Endoglucanase, Histone-like protein, Ribosomal proteins, five hypothetical proteins expressed only in the wild type strain, Lytic murein transglycosylase, Lipoprotein, Leucyl-tRNA synthetase, Co-chaperonin, Toluene tolerance, C-type cytochrome biogenesis membrane protein, Aminopeptidase and two hypothetical proteins expressed only in the <em>ΔhrpB4 </em>mutant. Furthermore, Peptidoglycan-associated outer membrane protein, Regulator of pathogenicity factor, Outer membrane proteins, Endopolygalacturonase, Chorismate mutase, Peptidyl-prolyl cis-trans isomerase and seven hypothetical proteins were detected in both strains, suggesting that there was no relationship with the secretion mediated by the type III secretory system, which is not functional in the mutant strain. Also worth mentioning is the Elongation factor Tu (EF-Tu), expressed only the wild type strain, and Type IV pilus assembly protein, Flagellin (FliC) and Flagellar hook-associated protein, identified in the wild-type strain secretome when grown only in NB. Noteworthy, that FliC, EF-Tu are classically characterized as PAMPs (Pathogen-associated molecular patterns), responsible for a PAMP-triggered immunity response. Therefore, our results highlight proteins potentially involved with the virulence. Overall, we conclude that the use of secretome data is a valuable approach that may bring more knowledge of the biology of this important plant pathogen, which ultimately can lead to the establishment of new strategies to combat citrus canker.</p>
Mass spectrometry proteomics data obtained from analysis of the secretome of Anisakis simplex (sensu stricto) L3 larvae.
<p>Mass spectrometry proteomics data obtained from analysis of the secretome of <em>Anisakis simplex</em> (sensu stricto) L3 larvae.</p>
Senescent preosteoclast secretome promotes metabolic syndrome-associated osteoarthritis through COX2-PGE2
<p><span>Metabolic syndrome–associated osteoarthritis (MetS-OA)</span><span> is a distinct osteoarthritis phenotype defined by the coexistence of MetS or its individual components. Despite the high prevalence of MetS-OA, its pathogenic mechanisms are unclear. Here, we report that humans and mice with MetS are more likely to develop osteoarthritis-related subchondral bone alterations than those without MetS. </span><span>MetS-OA mice exhibited</span><span> a rapid</span> <span>increase in joint </span><span>subchondral bone plate and trabecular thickness </span><span>before articular cartilage degeneration. Subchondral preosteoclasts undergo senescence </span><span>at the pre- or early</span><span>-osteoarthritis stage</span><span> and </span><span>acquire a unique secretome to</span><span> stimulate osteoblast differentiation and inhibit osteoclast differentiation. Antagonizing preosteoclast senescence markedly mitigates pathological subchondral alterations and osteoarthritis progression in MetS-OA mice. </span><span>At the molecular level,</span> <span>preosteoclast secretome activates </span><span>COX2-PGE2, resulting in stimulated differentiation of osteoblast progenitors for subchondral bone formation. Administration of a selective COX2 inhibitor attenuated subchondral bone alteration and osteoarthritis progression in MetS-OA mice. Longitudinal analyses of the human Osteoarthritis Initiative (OAI) cohort dataset also revealed that </span><span>COX2 inhibitor use, relative to non-selective nonsteroidal anti-inflammatory drug use</span><span>, is associated with less</span><span> progression of </span><span>osteoarthritis and subchondral bone marrow lesion worsening in participants with MetS-OA. Our findings suggest a central role of a senescent preosteoclast secretome-COX2/PGE2 axis in the pathogenesis of MetS-OA.</span></p>
Source files supporting "Nanoparticles Dysregulate the Human Placental Secretome with Consequences on Angiogenesis and Vascularization"
<p>Research data supporting the publication: Dugershaw-Kurzer, B. et al., 2024, "Nanoparticles Dysregulate the Human Placental Secretome with Consequences on Angiogenesis and Vascularization", Advanced Sciences. https://doi.org/10.1002/advs.202401060</p>
Raw Data for the article: High-Resolution Secretome Analysis of Chemical Hypoxia Treated Cells Identifies Putative Biomarkers of Chondrosarcoma
<p>Chondrosarcoma is the second most common bone tumor, accounting for 20% of all cases. Little is known about the pathology and molecular mechanisms involved in the development and in the metastatic process of chondrosarcoma. As a consequence, there are no approved therapies for this tumor and surgical resection is the only treatment currently available. Moreover, there are no available biomarkers for this type of tumor, and chondrosarcoma classification relies on operator-dependent histopathological assessment. Reliable biomarkers of chondrosarcoma are urgently needed, as well as greater understanding of the molecular mechanisms of its development for translational purposes. Hypoxia is a central feature of chondrosarcoma progression. The hypoxic tumor microenvironment of chondrosarcoma triggers a number of cellular events, culminating in increased invasiveness and migratory capability. Herein, we analyzed the effects of chemically-induced hypoxia on the secretome of SW 1353, a human chondrosarcoma cell line, using high-resolution quantitative proteomics. We found that hypoxia induced unconventional protein secretion and the release of proteins associated to exosomes. Among these proteins, which may be used to monitor chondrosarcoma development, we validated the increased secretion in response to hypoxia of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme well-known for its different functional roles in a wide range of tumors. In conclusion, by analyzing the changes induced by hypoxia in the secretome of chondrosarcoma cells, we identified molecular mechanisms that can play a role in chondrosarcoma progression and pinpointed proteins, including GAPDH, that may be developed as potential biomarkers for the diagnosis and therapeutic management of chondrosarcoma.</p>
Effectiveness of PRP, Conditioned Medium UC-MSCs Secretome and Hyaluronic Acid for the Treatment of Knee Osteoarthritis
ClinicalTrials.gov study NCT05579665. IPD Sharing: NO. Countries: 1. Publications: 6.
Secretome dataset for: The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence
Open the record for dataset details and reuse information.
Senescent preosteoclast secretome promotes metabolic syndrome-associated osteoarthritis through COX2-PGE2
Open the record for dataset details and reuse information.
The effector secretome of the Irish potato famine pathogen Phytophthora infestans
<p>Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes. Haas et al. (2009) reported the sequence of the 240 megabases (Mb) genome of P. infestans. In this dataset we provide an annotated list of candidate effectors that we identified in the proteome of P. infestans T30-4 (Haas et al. 2009). We have frozen this list since 2015 and we reference all the effectors with “PITG_xxxxx” numbers from this list. The proteins can be cross-referenced to the GenBank sequences using these PITG_xxxxx numbers. The matching GenBank accession for the genome assembly is GCA_000142945.1. We also provide here the assembly and gtf files.</p> <p>Reference:</p> <p><a href="https://kamounlab.dreamhosters.com/pdfs/Nature_09.pdf">Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H.Y., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T.O., Ah-Fong, A.M.V., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bollmann, S.R., Bos, J.I.B., Bulone, V., Cai, G., Cakir, C., Carrington, J.C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M.A., Fugelstad, J., Gilroy, E.M., Gnerre, S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Grunwald, N.J., Horn, K., Horner, N.R., Hu, C.-H., Huitema, E., Jeong, D.-H., Jones, A.M.E., Jones, J.D.G., Jones, R.W., Karlsson, E.K., Kunjeti, S.G., Lamour, K., Liu, Z., Ma, L., MacLean, D., Chibucos, M.C., McDonald, H., McWalters, J., Meijer, H.J.G., Morgan, W., Morris, P.F., Munro, C.A., O'Neill, K., Ospina-Giraldo, M., Pinzon, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D.J., Sykes, S., Thines, M., van de Vondervoort, P.J.I., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R.J., Whisson, S.C., Judelson, H.S., and Nusbaum, C. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461:393-398.</a></p>
Complete workflow for the prediction of the secretome of Fusarium oxysporum f. sp. albedinis, the causal agent of palm dieback
<p>Custom scripts for mining the secretome of <em>Fusarium oxysporum</em> f. sp. <em>albedinis</em>, the causal agent of date palm dieback disease. </p>
Dataset related to "Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution"
<p>Three .zip files contain the PDB files, mature protein sequences (without predicted signal peptides), and corresponding JSON files from AlphaFold2 containing pLDDT scores.</p> <p>Two .output files contain the all-vs-all sequence and structural similarity scores.</p>
Fig. 4 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses
Fig. 4. Physicochemical assessment of the grasspea suspension secretome (GSS), including pI (A), molecular weight (in kDa) (B), and hydrophilicity (C), with respect to MSS, DSS and LSS (MSS corresponds to the monocot suspension secretome, DSS to the dicot suspension secretome and LSS to the lower plant suspension secretome).
Fig. 2 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses
Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments.
Fig. 3 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses
Fig. 3. Overview of total grasspea suspension secreted (GSS) proteins and prediction of mode of secretion and (A) localization using multiple tools (B). Comparison of shared and distinct GSS proteins, first (C) with respect to total in vitro secretome (IVS) and in planta secretome (IPS) and second (D) compared to the in vitro suspension culture secretome reported in monocots, dicots, and lower plants, abbreviated as MSS, DSS and LSS, respectively (MSS corresponds to monocot suspension secretome, DSS to dicot suspension secretome and LSS to lower plant suspension secretome).
Fig. 1 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses
Fig. 1. Schematic representation of the experimental design and workflow of the establishment of the grasspea suspension secretome (GSS). Proteomic profiling was accomplished by generating suspension culture and sequential assessment of physicochemical properties and protein identification.
Fig. 6 in Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses
Fig. 6. Localization validation of endochitinase (S597) and G-type lectin S-receptor-like serine threonine kinase (S718). The panels include (A) expression of YFPtagged S597 in onion epidermal cells, (B) plasmolysis of S597-transformed onion peel (C), expression of YFP-tagged S718 in onion peel cells and (D) plasmolyzed onion peel cells expressing YFP-tagged S718. A pSITE3CA empty vector control was also monitored besides the target genes (E).
The Effects of Mesenchymal Stem Cell Secretome in Lupus Patients
ClinicalTrials.gov study NCT05921058. IPD Sharing: NO. Countries: 1. Publications: 2.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.